Merge branch 'yaml_load_and_save' of ssh://localhost:9001/gitroot/eodev/eodev

eo/app/gprop/mlp.h

@@ -20,6 +20,10 @@
 #include <assert.h>
 #include <limits>
 
+#ifdef HAVE_LIBYAML_CPP
+#include <yaml-cpp/serializable.h>
+#endif // HAVE_LIBYAML_CPP
+
 
 namespace mlp
 {
@@ -125,6 +129,21 @@ namespace mlp
       if ( probability >= 1.0 || rng.uniform() < probability)
 	perturb_num(bias, magnitude);
     }
+
+    #ifdef HAVE_LIBYAML_CPP
+    YAML_SERIALIZABLE_AUTO(neuron)
+    void emit_yaml(YAML::Emitter&out) const {
+            out << YAML::BeginMap;
+            out << YAML::Key << "Class" << YAML::Value << "mlp::neuron";
+            YAML_EMIT_MEMBER(out,bias);
+            YAML_EMIT_MEMBER(out,weight);
+            out << YAML::EndMap;
+    }
+    void load_yaml(const YAML::Node& node) {
+        YAML_LOAD_MEMBER(node, bias);
+        YAML_LOAD_MEMBER(node, weight);
+    }
+    #endif
  };
 }
 
@@ -140,8 +159,10 @@ namespace std {
     return is >> n.bias >> n.weight;
   }
 
+
 }
 
+
 namespace mlp {
 
   //---------------------------------------------------------------------------
@@ -190,6 +211,21 @@ namespace mlp {
       for(iterator n = begin(); n != end(); ++n)
 	n->perturb();
     }
+    #ifdef HAVE_LIBYAML_CPP
+    friend ostream& operator<<(YAML::Emitter& e, const layer &l) {
+        e << ((std::vector<neuron>)l);
+    }
+
+    friend void operator>>(const YAML::Node& n, layer &l) {
+        // These temporary variable shenanegins are necessary because 
+        // the compiler gets very confused about which template operator>> 
+        // function to use.
+        // The following does not work:  n >> l;
+        // So we use a temporary variable thusly:
+        std::vector<mlp::neuron> *obviously_a_vector = &l;
+        n >> *obviously_a_vector;
+    }
+    #endif
 
   };
 
@@ -222,6 +258,9 @@ namespace mlp {
   //---------------------------------------------------------------------------
 
   class net: public std::vector<layer>
+  #ifdef HAVE_LIBYAML_CPP
+  , public YAML::Serializable
+  #endif
   {
   public:
     net(const unsigned& num_inputs = 0,
@@ -235,6 +274,18 @@ namespace mlp {
     net(istream &is) {
 	load(is);
     }
+    #ifdef HAVE_LIBYAML_CPP
+    YAML_SERIALIZABLE_AUTO(net)
+    void emit_members(YAML::Emitter&out) const {
+        const std::vector<layer>* me_as_layer_vector = this;
+        out << YAML::Key << "layers" << YAML::Value << *me_as_layer_vector;
+    }
+
+    void load_members(const YAML::Node& node) {
+        std::vector<layer>* me_as_layer_vector = this;
+        node["layers"] >> *me_as_layer_vector;
+    }
+    #endif // HAVE_LIBYAML_CPP  
 
       /** Virtual destructor */
       virtual ~net() {};
@@ -305,10 +356,13 @@ namespace mlp {
         for(const_iterator l = begin(); l != end(); ++l)
 	   os << l->size() << " ";
         os << "\n";
-	os << *this;
+        os << "< ";
-        os << "\n";
+        for(const_iterator l = begin(); l != end(); ++l)
+	   os << *l << " ";
+        os << ">\n";
     }
 
+
     unsigned num_inputs()  const { return front().front().length() - 1; }
     unsigned num_outputs() const { return back().size(); }
     unsigned num_hidden_layers() const {

eo/configure.in

@@ -38,6 +38,22 @@ AC_TYPE_SIZE_T
 dnl Checks for libraries and library functions.
 AC_CHECK_LIB(m, cos)
 
+
+dnl Check for C++ library yaml-cpp (AC_CHEC_LIB only supports checking for C libraries)
+AC_MSG_CHECKING('libyaml-cpp available')
+AC_LANG(C++)
+SAVED_LDFLAGS=$LDFLAGS
+LDFLAGS="$LDFLAGS -lyaml-cpp"
+AC_LINK_IFELSE(
+    [AC_LANG_PROGRAM([#include <yaml-cpp/yaml.h>], [YAML::Emitter  dummy])],
+        [ AC_MSG_RESULT([yes])
+          SAVED_LDFLAGS="$SAVED_LDFLAGS -lyaml-cpp"
+          AC_DEFINE(HAVE_LIBYAML_CPP,1,[Define to 1 if you have libyaml-cpp installed]) ],
+        [AC_MSG_RESULT([no])])
+LDFLAGS=$SAVED_LDFLAGS
+
+
+
 dnl user-switches
 AC_APPLICATIONS
 AC_DEBUG

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eo/tutorial/html/index.html

@@ -1,199 +0,0 @@
-<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
-<html>
-<head>
-   <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
-   <meta name="GENERATOR" content="Mozilla/4.75 [en] (X11; U; Linux 2.2.17-21mdk i686) [Netscape]">
-   <title>Tutorial EO</title>
-</head>
-<body text="#000000" link="#0000EF" vlink="#51188E" alink="#FF0000" background="beige009.jpg">
-<a href="eoTopDown.html">Algorithm-Based</a> - <a href="eoBottomUp.html">Component-Based</a>
-- <a href="eoProgramming.html">Programming hints</a> - <b><font face="Arial,Helvetica"><font size=+1><a href="../../doc/html/index.html">EO
-documentation</a></font></font></b>
-<hr WIDTH="100%">
-<center><b><font color="#FF0000">Welcome to EO, the Evolving Objects library,
-and to</font></b>
-<b><font color="#FF0000"></font></b>&nbsp;
-<h1>
-<font color="#FF0000">EO Tutorial</font></h1></center>
-
-<center><font color="#FF0000">Version 0.92 - Jan. 5 2001</font></center>
-
-<p>The short term idea of this tutorial is to help you <font color="#FF6600">build
-your own Evolutionary Algorithms</font> using EO - while the long term
-idea is that you will be able to contribute to EO, and ultimately write
-<font color="#FF6600">our</font>
-EAs :-)
-<h3>
-
-<hr WIDTH="100%"><b><font color="#000099"><font size=+2>About this tutorial</font></font></b></h3>
-This tutorial can be used in 2 different ways: algorithm-based and component-based.
-<ul>
-<li>
-<a href="eoTopDown.html">Algorithm-Based</a> means you start from a <font color="#FF6600">very
-simple, ready-to-run algorithm,</font> and gradually modify it, making
-it both more powerful and more complex.</li>
-
-<li>
-<a href="eoBottomUp.html">Component-Based</a> means you start by examining
-the
-<font color="#FF6600">components of an EA one by one</font>, down to
-the level of complexity you feel comfortable with, and then build the whole
-algorithm using those components you need (or the one you are mastering).
-Such approach might be viewed as going through a simplified user guide,
-too.</li>
-</ul>
-However, it is <b><font color="#FF6600">strongly recommended</font></b>
-that you take some time on the first lesson of the Algorithm-Based approach
-to get familiar with the basic concepts that are used throughout EO. Anyway,
-as of today, December 19, the Component-Based is only very sparsely written
-:-)
-<p>
-<hr WIDTH="100%"><b><font color="#000099"><font size=+2>Links and Related
-documents</font></font></b>
-<ul>
-<li>
-There are of course a few (very few) <a href="eoProgramming.html">programming
-hints</a> that you should know.</li>
-
-<li>
-THe <a href="../../doc/html/index.html">EO documentation </a>- automatically
-generated from the comments in the code - is very helpful to get an idea
-of the <b><font color="#FF6600">inheritance diagrams</font></b> of EO classes,
-and to quickly reach some specific part of the code.</li>
-
-<br>The top page of each class documentation is for instance the inheritance
-diagram of the class, and you'll learn a lot by simply looking at it.
-<li>
-And, last but not least, we assume you know approximately that an Evolutionary
-Algorithm looks like this, but otherwise you can try this <a href="eoIntroEA.html">very
-brief introduction</a> (not written yet, Jan. 2001, sorry).</li>
-</ul>
-
-<p><br>
-<hr WIDTH="100%"><b><font color="#000099"><font size=+2>Colors and navigation:</font></font></b>
-<p>You will see this diagram in quite many places, as for instance at the
-top of all examples - usually it will be clickable and will help you navigate
-among the different parts of an EO program. See the <a href="eoIntroEA.html">brief
-introduction to Evolutionary Computation</a> for a detailed explanation.
-<center>
-<p><img SRC="EA_tutorial.jpg" ></center>
-<a NAME="colors"></a>
-<p>But in the text itself, <b><font color="#FF6600">colors are important</font></b>,
-as they will be used throughout this tutorial to clearly mark which part
-of the algorithm we are discussing. So please keep in mind that, whereas
-<b><font color="#FF6600">orange
-is for emphasis</font></b>,
-<ul>
-<li>
-<b><font color="#999900">Yellowish</font></b> is for <b><font color="#999900">representation</font></b>,
-i.e. the choice of the <b><font color="#999900">genotype</font></b></li>
-
-<li>
-<font color="#CC33CC">Magenta</font> is for the <font color="#CC33CC">stochastic
-operators</font> that are <b><font color="#999900">representation-dependent</font>,</b>
-i.e. <font color="#CC33CC">initialisation</font> and variation operators
-(<font color="#CC33CC">crossover</font>, <font color="#CC33CC">mutation</font>
-and the like).</li>
-
-<li>
-<font color="#009900">Green</font> is for the implementation of <font color="#009900">Darwinism</font>,
-i.e. the way the individuals are <font color="#009900">selected</font>
-for reproduction and <font color="#009900">survive.</font></li>
-
-<li>
-<font color="#CC0000">Red</font> is for evaluation, i.e. the computation
-of the <font color="#CC0000">fitness</font> of all individuals</li>
-
-<li>
-<font color="#3366FF">Blue</font> is for interactions of the user and the
-program, as for instance choice of <font color="#3366FF">stopping criterion</font>,
-on-line display of nice <font color="#3366FF">statistics</font> or initial
-<font color="#3366FF">choice
-of all program parameters</font>.</li>
-
-<li>
-<font color="#993300">Brown</font> is for everything that is NOT part of
-any of the above, i.e. random number generator, or basic C++/STL syntax
-.</li>
-
-<li>
-Note that <font color="#FF6666">pink</font> will be used to describe the
-syntax of compile orders (i.e. at the operating system level, see e.g.
-<a href="#install">below</a>).</li>
-
-<li>
-<b><font face="Arial,Helvetica"><font size=+1>Last, but not least, all
-links into EO documentation will use the Helvetica typeface, like this
-line you are now reading.</font></font></b></li>
-</ul>
-
-<hr WIDTH="100%"><b><font color="#000099"><font size=+1>This tutorial is
-not</font></font></b>
-<ul>
-<li>
-A course on Evolutionary Computation. You can find such things on the Internet,
-maybe you can start <a href="http://www.wi.leidenuniv.nl/~gusz/Flying_Circus/">here.</a></li>
-
-<li>
-An interface that would allow you to build your Evolutionary Programs by
-a few clicks; such a thing does exist, is called <a href="http://www-rocq.inria.fr/EASEA/">EASEA</a>,
-and is complementary to this tutorial as it helps the user to build some
-simple EO programs from simple description. But there are things that EASEA
-cannot do, and you will have to do it yourself and will need to increase
-your knowledge about EO for that - hence this tutorial.</li>
-
-<li>
-A coffee machine - though you might want to spend some time here when you're
-tired of everything else, to improve your knowledge of EO slowly and gradually
-rather than when you have something urgent to code :-)</li>
-</ul>
-
-<hr WIDTH="100%"><a NAME="install"></a><b><font color="#000099"><font size=+1>Before
-you start</font></font></b>
-<p>You should of course have downloaded and installed the whole <a href="http://www.sourceforge.net/projects/eodev">EO
-library</a> (how did you get this file if not???).
-<br>So we'll assume that you are now in the Tutorial directory, and that
-your prompt looks something like
-<p><b><tt><font color="#FF6666">(myname@myhost) EOdir/Tutorial %</font></tt></b>
-<p>so you should now type in
-<p><b><tt><font color="#FF6666">make lesson1</font></tt></b>
-<p>and see something like
-<p><font face="Courier New,Courier"><font color="#000000">(myname@myhost)
-EOdir/Tutorial % make lesson1</font></font>
-<br><b><tt><font color="#FF6666">c++ -DPACKAGE=\"eo\" -DVERSION=\"0.9.1\"
--I. -I../../src -Wall -g -c FirstBitGA.cpp</font></tt></b>
-<br><b><tt><font color="#FF6666">c++ -Wall -g -o FirstBitGA FirstBitGA.o
-../../src/libeo.a ../../src/utils/libeoutils.a</font></tt></b>
-<br><b><tt><font color="#FF6666">c++ -DPACKAGE=\"eo\" -DVERSION=\"0.9.1\"
--I. -I../../src -Wall -g -c FirstRealGA.cpp</font></tt></b>
-<br><b><tt><font color="#FF6666">c++ -Wall -g -o FirstRealGA FirstRealGA.o
-../../src/libeo.a ../../src/utils/libeoutils.a</font></tt></b>
-<p>and two now executable files should have appeared in the subdirectory
-Lesson1, namely <b><tt><font color="#990000">FirstBitGA</font></tt></b>
-and <b><tt><font color="#990000">FirstRealGA</font></tt></b> (see <a href="eoLesson1.html">First
-lesson</a> to know more about these two ready-to-run programs). If this
-doesn't work, please go back to the main EO directory and run the installation
-program.
-<p>You should also test that you can access the EO documentation in the
-menu line below: you might not need to go there immediately, but just in
-case you make rapid progress ... This menu bar should be on all pages of
-this tutorial, allowing you to navigate easily.
-<p>Last, but not least: EO is improving only&nbsp; from the good will of
-contributors. This is also true for this tutorial: If you find anything
-that you think could be improved, you are welcome to <a href="mailto:Marc.Schoenauer@polytechnique.fr">e-mail
-me</a>.
-<center>
-<p><font color="#000099"><font size=+2>Enjoy!
-<hr WIDTH="100%"></font></font><a href="eoTopDown.html">Algorithm-Based</a>
-- <a href="eoBottomUp.html">Component-Based</a> - <a href="eoProgramming.html">Programming
-hints</a> -<b><font size=+1> <font face="Arial,Helvetica"><a href="../../doc/html/index.html">EO
-documentation</a></font></font></b></center>
-
-<hr>
-<address>
-<a href="mailto:Marc.Schoenauer@polytechnique.fr">Marc Schoenauer</a></address>
-
-<br><!-- Created: Mon Oct 30 07:27:13 CET 2000 --><!-- hhmts start -->Last
-modified: Fri Nov 28 2000&nbsp;<!-- hhmts end -->
-</body>
-</html>